AMBER Archive (2009)

Subject: Re: [AMBER] catenan simulation problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Mar 06 2009 - 08:59:24 CST

On Fri, Mar 06, 2009, Cristina Sisu wrote:
>
> I want to simulate a catenan. In the first instance I created a mol2
> file using antechamber. I submitted it to leap and managed to get the
> topology and coordinate files for both vacuum form and solvated
> molecule. However if I check the pdb file of the solvated molecule I
> notice that the molecule was split. The first ring is labelled correctly
> but the second ring is split in trio (like water) and the last 100 water
> molecules are treated as one single molecule. To be more specific it
> looks like this:

How did you create the pdb file? Can you list the exact commands you
used in antechamber and leap, or provide the mol2 file? Maybe if we can
reproduce the problem we can see what is going wrong.

...thanks...dac

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